{"id":"https://openalex.org/W4385763856","doi":"https://doi.org/10.24963/ijcai.2023/744","title":"Graph-based Molecular Representation Learning","display_name":"Graph-based Molecular Representation Learning","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385763856","doi":"https://doi.org/10.24963/ijcai.2023/744"},"language":"en","primary_location":{"id":"doi:10.24963/ijcai.2023/744","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/744","pdf_url":"https://www.ijcai.org/proceedings/2023/0744.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.ijcai.org/proceedings/2023/0744.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100932875","display_name":"Zhichun Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhichun Guo","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070509358","display_name":"Kehan Guo","orcid":"https://orcid.org/0009-0004-6396-1869"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kehan Guo","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023104692","display_name":"Bozhao Nan","orcid":"https://orcid.org/0000-0001-9645-0724"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bozhao Nan","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103057036","display_name":"Yijun Tian","orcid":"https://orcid.org/0000-0001-9831-7927"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yijun Tian","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008097291","display_name":"Roshni G. Iyer","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roshni G. Iyer","raw_affiliation_strings":["University of California, Los Angeles","University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088825137","display_name":"Yihong Ma","orcid":"https://orcid.org/0000-0001-8710-4707"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yihong Ma","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029114040","display_name":"Olaf Wiest","orcid":"https://orcid.org/0000-0001-9316-7720"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olaf Wiest","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000755750","display_name":"Xiangliang Zhang","orcid":"https://orcid.org/0000-0002-3574-5665"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiangliang Zhang","raw_affiliation_strings":["University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I2799798094","display_name":"UCLA Health","ror":"https://ror.org/01d88se56","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799798094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["UCLA","University of California, Los Angeles"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA","institution_ids":["https://openalex.org/I2799798094"]},{"raw_affiliation_string":"University of California, Los Angeles","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022275632","display_name":"Chuxu Zhang","orcid":"https://orcid.org/0000-0002-8349-7926"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chuxu Zhang","raw_affiliation_strings":["Brandeis University","Brandeis University {zguo5,kguo2,bnan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brandeis University","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Brandeis University {zguo5,kguo2,bnan,","institution_ids":["https://openalex.org/I6902469"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068157871","display_name":"Nitesh V. Chawla","orcid":"https://orcid.org/0000-0003-3932-5956"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]},{"id":"https://openalex.org/I3132061591","display_name":"Notre Dame of Dadiangas University","ror":"https://ror.org/009yjbg58","country_code":"PH","type":"education","lineage":["https://openalex.org/I3132061591"]}],"countries":["PH","US"],"is_corresponding":false,"raw_author_name":"Nitesh V. Chawla","raw_affiliation_strings":["Notre Dame","University of Notre Dame"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Notre Dame","institution_ids":["https://openalex.org/I3132061591"]},{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":10.5175,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.98705189,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"6638","last_page":"6646"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12327","display_name":"Various Chemistry Research Topics","score":0.9848999977111816,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7302165627479553},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.6750244498252869},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.663730263710022},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5422201752662659},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5410538911819458},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.49571311473846436},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.4934317171573639},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4854944050312042},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.47855454683303833},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4721527099609375},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4443926513195038},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3200855255126953}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7302165627479553},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.6750244498252869},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.663730263710022},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5422201752662659},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5410538911819458},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.49571311473846436},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4934317171573639},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4854944050312042},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47855454683303833},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4721527099609375},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4443926513195038},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3200855255126953},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.24963/ijcai.2023/744","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/744","pdf_url":"https://www.ijcai.org/proceedings/2023/0744.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.24963/ijcai.2023/744","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/744","pdf_url":"https://www.ijcai.org/proceedings/2023/0744.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G1696205824","display_name":null,"funder_award_id":"CHE-2202693","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G356514451","display_name":"NSF Center for Computer-Assisted Synthesis","funder_award_id":"2202693","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5350220339","display_name":null,"funder_award_id":"2202693","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G6073209943","display_name":null,"funder_award_id":"CHE-2202693","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385763856.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W29374554","https://openalex.org/W1757990252","https://openalex.org/W2038702914","https://openalex.org/W2594183968","https://openalex.org/W2606363443","https://openalex.org/W2606780347","https://openalex.org/W2753921001","https://openalex.org/W2785942661","https://openalex.org/W2786722833","https://openalex.org/W2807792492","https://openalex.org/W2899070097","https://openalex.org/W2950898568","https://openalex.org/W2954380329","https://openalex.org/W2962711740","https://openalex.org/W2962876161","https://openalex.org/W2963396480","https://openalex.org/W2963662739","https://openalex.org/W2963676163","https://openalex.org/W2964015378","https://openalex.org/W2965857891","https://openalex.org/W2994860160","https://openalex.org/W3005111505","https://openalex.org/W3005552578","https://openalex.org/W3018495986","https://openalex.org/W3035011799","https://openalex.org/W3036737467","https://openalex.org/W3036974265","https://openalex.org/W3040246664","https://openalex.org/W3045928028","https://openalex.org/W3094060150","https://openalex.org/W3095602948","https://openalex.org/W3095883070","https://openalex.org/W3127113723","https://openalex.org/W3130274530","https://openalex.org/W3133498786","https://openalex.org/W3162011170","https://openalex.org/W3166086511","https://openalex.org/W3172495685","https://openalex.org/W3188887004","https://openalex.org/W3192905713","https://openalex.org/W3201083857","https://openalex.org/W3206711231","https://openalex.org/W3211477647","https://openalex.org/W3212362876","https://openalex.org/W3213940558","https://openalex.org/W3215452784","https://openalex.org/W4226075199","https://openalex.org/W4231645939","https://openalex.org/W4282004119","https://openalex.org/W4283212492","https://openalex.org/W4286907726","https://openalex.org/W4287126984","https://openalex.org/W4287828570","https://openalex.org/W4288275971","https://openalex.org/W4290875097","https://openalex.org/W4294558607","https://openalex.org/W4297733535","https://openalex.org/W4298089296","https://openalex.org/W4324122028","https://openalex.org/W4367047209","https://openalex.org/W4382239191"],"related_works":["https://openalex.org/W2165912799","https://openalex.org/W2735662278","https://openalex.org/W2382615723","https://openalex.org/W4311804456","https://openalex.org/W1987484445","https://openalex.org/W2623658258","https://openalex.org/W2143413548","https://openalex.org/W1969219540","https://openalex.org/W2370459448","https://openalex.org/W2808877228"],"abstract_inverted_index":{"Molecular":[0],"representation":[1,69],"learning":[2,14],"(MRL)":[3],"is":[4],"a":[5],"key":[6],"step":[7],"to":[8],"build":[9],"the":[10,27,36,72,82,124,131],"connection":[11],"between":[12],"machine":[13],"and":[15,30,86,93,126],"chemical":[16,75,109],"science.":[17],"In":[18,60],"particular,":[19],"it":[20],"encodes":[21],"molecules":[22],"as":[23],"numerical":[24],"vectors":[25],"preserving":[26],"molecular":[28,57,68,88],"structures":[29],"features,":[31],"on":[32,55,101,138],"top":[33],"of":[34,84],"which":[35],"downstream":[37],"tasks":[38],"(e.g.,":[39],"property":[40],"prediction)":[41],"can":[42],"be":[43],"performed.":[44],"Recently,":[45],"MRL":[46,95],"has":[47],"achieved":[48],"considerable":[49],"progress,":[50],"especially":[51,71],"in":[52,117,130],"methods":[53,73,96],"based":[54,100],"deep":[56],"graph":[58],"learning.":[59],"this":[61,118],"survey,":[62],"we":[63,79,91,105,121,134],"systematically":[64],"review":[65],"these":[66],"graph-based":[67],"techniques,":[70],"incorporating":[74],"domain":[76],"knowledge.":[77],"Specifically,":[78],"first":[80],"introduce":[81],"features":[83],"2D":[85],"3D":[87],"graphs.":[89],"Then":[90],"summarize":[92],"categorize":[94],"into":[97],"three":[98],"groups":[99],"their":[102],"input.":[103],"Furthermore,":[104],"discuss":[106],"some":[107],"typical":[108],"applications":[110],"supported":[111],"by":[112],"MRL.":[113],"To":[114],"facilitate":[115],"studies":[116],"fast-developing":[119],"area,":[120],"also":[122],"list":[123],"benchmarks":[125],"commonly":[127],"used":[128],"datasets":[129],"paper.":[132],"Finally,":[133],"share":[135],"our":[136],"thoughts":[137],"future":[139],"research":[140],"directions.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":27},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":5}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
